We use S-gene status by specimen date sourced from UKHSA as a direct proxy for the Omicron variant with a target failure indicating a case has the Omicron variant. Data was available by UKHSA region.
All models were implemented using the forecast.vocs R package[1,2] and fit using stan[3] and cmdstanr[4]. Each model was fit using 2 chains with each chain having 1000 warmup steps and 2000 sampling steps. Convergence was assessed using the Rhat diagnostic[3]. Models were compared using approximate leave-one-out (LOO) cross-validation[5,6] where negative values indicate an improved fit for the correlated model.
Daily cases in England and by UKHSA region, with S-gene target result (failed, confirmed detected, or unknown), and centred 7-day moving average up to date of data truncation (dotted line). Source: UKHSA and coronavirus.gov.uk; data by specimen date.
Daily fraction of those tested for S gene status with SGTF by UKHSA region on the logit scale. The dashed vertical lines indicate Mondays. Note that the data is by specimen date and more recent dates may be from an incomplete sample . Source: UKHSA
Daily fraction of those tested for S gene status with SGTF by UKHSA region on the logit scale. The dashed vertical lines indicate Mondays. Note that the data is by specimen date and more recent dates may be from an incomplete sample . Source: UKHSA
Developed by Sam Abbott, Katharine Sherratt, and Sebastian Funk